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new module hamronization/rgi (#1844)
* new module hamronization/rgi * remove comments * Update modules/hamronization/rgi/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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44
modules/hamronization/rgi/main.nf
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44
modules/hamronization/rgi/main.nf
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process HAMRONIZATION_RGI {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
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'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
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input:
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tuple val(meta), path(report)
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val(format)
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val(software_version)
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val(reference_db_version)
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output:
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tuple val(meta), path("*.json") , optional: true, emit: json
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tuple val(meta), path("*.tsv") , optional: true, emit: tsv
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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hamronize \\
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rgi \\
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${report} \\
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$args \\
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--format ${format} \\
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--analysis_software_version ${software_version} \\
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--reference_database_version ${reference_db_version} \\
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--input_file_name ${prefix} \\
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> ${prefix}.${format}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
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END_VERSIONS
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"""
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}
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62
modules/hamronization/rgi/meta.yml
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62
modules/hamronization/rgi/meta.yml
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name: "hamronization_rgi"
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description: Tool to convert and summarize RGI outputs using the hAMRonization specification.
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keywords:
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- amr
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- antimicrobial resistance
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- arg
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- antimicrobial resistance genes
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- reporting
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- rgi
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tools:
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- hamronization:
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description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
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homepage: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
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documentation: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
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tool_dev_url: "https://github.com/pha4ge/hAMRonization"
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doi: ""
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licence: "['GNU Lesser General Public v3 (LGPL v3)']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- report:
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type: file
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description: Output .txt file from RGI
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pattern: "*.txt"
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- format:
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type: value
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description: Type of report file to be produced
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pattern: "tsv|json"
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- software_version:
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type: value
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description: Version of DeepARG used
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pattern: "[0-9].[0-9].[0-9]"
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- reference_db_version:
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type: value
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description: Database version of DeepARG used
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pattern: "[0-9].[0-9].[0-9]"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- json:
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type: file
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description: hAMRonised report in JSON format
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pattern: "*.json"
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- tsv:
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type: file
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description: hAMRonised report in TSV format
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pattern: "*.json"
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authors:
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- "@louperelo"
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@ -1011,6 +1011,10 @@ hamronization/deeparg:
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- modules/hamronization/deeparg/**
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- modules/hamronization/deeparg/**
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- tests/modules/hamronization/deeparg/**
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- tests/modules/hamronization/deeparg/**
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hamronization/rgi:
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- modules/hamronization/rgi/**
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- tests/modules/hamronization/rgi/**
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hamronization/summarize:
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hamronization/summarize:
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- modules/hamronization/summarize/**
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- modules/hamronization/summarize/**
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- tests/modules/hamronization/summarize/**
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- tests/modules/hamronization/summarize/**
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16
tests/modules/hamronization/rgi/main.nf
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16
tests/modules/hamronization/rgi/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { RGI_MAIN } from '../../../../modules/rgi/main/main.nf'
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include { HAMRONIZATION_RGI } from '../../../../modules/hamronization/rgi/main.nf'
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workflow test_hamronization_rgi {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
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]
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RGI_MAIN ( input )
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HAMRONIZATION_RGI ( RGI_MAIN.out.tsv, 'tsv', '1.0.2', '3.2.3' )
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}
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5
tests/modules/hamronization/rgi/nextflow.config
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5
tests/modules/hamronization/rgi/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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8
tests/modules/hamronization/rgi/test.yml
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8
tests/modules/hamronization/rgi/test.yml
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- name: hamronization rgi
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command: nextflow run ./tests/modules/hamronization/rgi -entry test_hamronization_rgi -c ./tests/config/nextflow.config -c ./tests/modules/hamronization/rgi/nextflow.config
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tags:
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- hamronization
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- hamronization/rgi
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files:
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- path: output/hamronization/test.tsv
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md5sum: 3e0f7e9321afbc947dd1ea32ce9c0559
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